Inconsistencies and questions (spoilers-inside)

I'm just back from seeing the film and I have mixed feelings. I really enjoyed the film up until the scene where the snake-like creature breaks the biologist's arm and the geologist's face is melted. OK, so the scene in Scotland was a little pointless, the main female character's boyfriend was a total ass-hat and some of the plot devices were a little shoehorned in (I'm looking at you, medical surgery pod and lifeboat) but I thought the suspense was built well and the first sight of that snake creature, with it's wings opening like a facehugger's fingers filled me with excitement. I was all teed up for a true horror classic. Then it went downhill fast. The scene with the squid caesarian made me cringe for the wrong reason, the "black ooze" had far too many different effects on people for me to keep track of and noone seemed to be that phased by the whole ordeal (no "game over man, game over" moments). The dialogue was crap, I couldn't understand why they didn't just cast an old man as Weyland, rather than use obvious makeup to make a young man appear old, and there were far too many characters (why did they need not one but two copilots who only appeared in a couple of scenes?). The most annoying bit, though, was the inconsistencies. Why did they make such a big deal of putting a gash into the side of the spacecraft and showing the "Alien" at the end? Two things that point at the spacecraft being the "derelict" from the first movie. The space jockey doesn't die in his seat and this is not LV426 so it can't be the derelict. It's just confused. It feels like they couldn't decide whether to make it a proper prequel to alien or leave the door open for the sequel so they hashed an ending together to try and be all things to all people. They should have had the spacecraft limp into space after the prometheus gashes the hull and then had the spacejockey's chest burst, causing the ship to crash on an unknown world...LV426. Argh, it showed so much promise and then fell short.